Hydrophobic Cluster Analysis Reveals a Third Chromodomain in theTetrahymenaPdd1p Protein of the Chromo Superfamily

The protein Pdd1p (for programmed DNA degradation) links heterochromatin assembly and DNA elimination in Tetrahymena and has recently been identified as a new member of the chromo superfamily that contains two chromodomains. Using the sensitive bidimensional Hydrophobic Cluster Analysis (HCA) method, we have identified a third, highly divergent chromodomain in the Pdd1p sequence. Based on similarity to chromo shadow domains that mediate protein-protein interactions, this newly identified chromodomain may direct the binding of Pdd1p to other proteins. These findings suggest that Pdd1p may be the prototypical member of a new class in the chromo superfamily as all other members contain only one or two chromodomains. The results also demonstrate the power of HCA in identifying relationships which are not detected by conventional methods of sequence analysis.